Summary
Cheminformatics
This metapackage will install cheminformatics packages
useful for chemists.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for DebiChem
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the DebiChem mailing list
Links to other tasks
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DebiChem Cheminformatics packages
Official Debian packages with high relevance
Libcdk-java
Chemistry Development Kit (CDK) Java libraries
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Versions of package libcdk-java |
Release | Version | Architectures |
jessie | 1.2.10-6 | all |
wheezy | 1.2.10-3 | all |
squeeze | 1.0.2-5 | all |
sid | 1.2.10-8 | all |
bullseye | 1.2.10-8 | all |
buster | 1.2.10-7 | all |
stretch | 1.2.10-6 | all |
upstream | 2.3 |
Debtags of package libcdk-java: |
devel | lang:java, library |
field | chemistry |
role | devel-lib |
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License: DFSG free
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The CDK is a library of Java classes used in computational and
information chemistry and in bioinformatics. It includes renderers,
file IO, SMILES generation/parsing, maximal common substructure
algorithms, fingerprinting and much, much more.
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Libopsin-java
Chemical name to structure converter
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Versions of package libopsin-java |
Release | Version | Architectures |
stretch | 1.5.0-1 | all |
buster | 2.3.1-1 | all |
jessie | 1.5.0-1 | all |
bullseye | 2.4.0-2 | all |
sid | 2.4.0-2 | all |
wheezy | 1.2.0-1 | all |
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License: DFSG free
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OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound
names to semantic chemical information and outputs a structure either as
CML (Chemical Markup Language), SMILES, or InChI.
This package contains the Java library.
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Openbabel
Chemical toolbox utilities (cli)
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Versions of package openbabel |
Release | Version | Architectures |
squeeze | 2.2.3-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
stretch | 2.3.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.2+dfsg-2 | amd64,armel,armhf,i386 |
wheezy | 2.3.1+dfsg-4 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
experimental | 3.0.0+dfsg-1 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
sid | 2.4.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.4.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 3.0.0 |
Debtags of package openbabel: |
field | chemistry |
interface | commandline |
role | program |
scope | utility |
use | converting |
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License: DFSG free
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Open Babel is a chemical toolbox designed to speak the many languages of
chemical data. It allows one to search, convert, analyze, or store data from
molecular modeling, chemistry, solid-state materials, biochemistry, or related
areas. Features include:
- Hydrogen addition and deletion
- Support for Molecular Mechanics
- Support for SMARTS molecular matching syntax
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Flexible atom typer and perception of multiple bonds from atomic coordinates
- Gasteiger-Marsili partial charge calculation
File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL
Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.
This package includes the following utilities:
- babel: Convert between various chemical file formats
- obenergy: Calculate the energy for a molecule
- obminimize: Optimize the geometry, minimize the energy for a molecule
- obgrep: Molecular search program using SMARTS pattern
- obgen: Generate 3D coordinates for a molecule
- obprop: Print standard molecular properties
- obfit: Superimpose two molecules based on a pattern
- obrotamer: Generate conformer/rotamer coordinates
- obconformer: Generate low-energy conformers
- obchiral: Print molecular chirality information
- obrotate: Rotate dihedral angle of molecules in batch mode
- obprobe: Create electrostatic probe grid
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Python-chemfp
cheminformatics fingerprints file formats and tools
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Versions of package python-chemfp |
Release | Version | Architectures |
wheezy | 1.0-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 1.1p1-2.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.1p1-2.1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.1p1-2.1 | amd64,armel,i386,mips64el,ppc64el,s390x |
stretch | 1.1p1-2.1 | amd64,armel,i386,mips64el,ppc64el,s390x |
jessie | 1.1p1-2.1 | amd64,armel,armhf,i386 |
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License: DFSG free
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Chem-fingerprints is a set of formats and related tools for the storage,
exchange, and search of cheminformatics fingerprint data sets.
It translates fingerprints from the OpenBabel and RDKIT and
cheminformatics packages (as well as the proprietary OEChem package)
into the binary FPS format.
Besides Python modules, it provides the following tools:
- sdf2fps - Extract fingerprint data from SD tags
- ob2fps - Use OpenBabel to generate fingerprints from structures
- rdkit2fps - Use RDKit to generate fingerprints from structures
- oe2fps - Use OEChem/OEGraphSim to generate fingerprints from structures
- simsearch - Do threshold or k-nearest neighbor Tanimoto similarity searches
between two FPS files
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Python-cinfony
Python abstraction layer to cheminformatics toolkits
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Versions of package python-cinfony |
Release | Version | Architectures |
buster | 1.2-1 | all |
stretch | 1.2-1 | all |
jessie | 1.2-1 | all |
sid | 1.2-4 | all |
wheezy | 1.1-1 | all |
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License: DFSG free
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Cinfony provides a common Python interface to various cheminformatics
toolkits. This makes it possible to use the complementary features of
cheminformatics toolkits using a common interface. If functionality is
provided by more than one toolkit, the Cinfony user can choose the
implementation they prefer.
Cinfony supports the following toolkits:
- OpenBabel
- RDKit
- CDK
- Indigo
Cinfony also includes the Opsin module for translating IUPAC names to chemical
data and the Webel web services module.
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Python-fmcs
Find Maximum Common Substructure
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Versions of package python-fmcs |
Release | Version | Architectures |
wheezy | 1.0-1 | all |
jessie | 1.0-1 | all |
stretch | 1.0-1 | all |
buster | 1.0-1 | all |
sid | 1.0-1 | all |
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License: DFSG free
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Fcms finds the maximum common substructure (MCS) of a group (or cluster) of
chemical structures and report the result as a SMARTS string.
More specifically, the MCS found is a common edge subgraph, and not a
common induced subgraph. Only connected MCSes are found.
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Python-indigo
Organic Chemistry Toolkit (Python module)
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Versions of package python-indigo |
Release | Version | Architectures |
sid | 1.2.3-1 | all |
buster | 1.2.3-1 | all |
stretch | 1.1.12-2 | all |
jessie | 1.1.12-1 | all |
wheezy | 1.0.0-2 | all |
bullseye | 1.2.3-1 | all |
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License: DFSG free
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Indigo is a C++ based organic chemistry and cheminformatics software
environment. Features Include:
- Molecule and reaction rendering including SVG support
- Automatic layout for SMILES-represented molecules and reactions
- Canonical (isomeric) SMILES computation
- Exact matching, substructure matching, SMARTS matching
- Matching of tautomers and resonance structures
- Molecule fingerprinting, molecule similarity computation
- Fast enumeration of SSSR rings, subtrees, and edge sugraphs
- Molecular weight, molecular formula computation
- R-Group deconvolution and scaffold detection
- Computation of the exact maximum common substructure for an
arbitrary amount of input structures
- Combinatorial chemistry
- Plugin support in the API
File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
SMARTS.
This package contains the Python modules.
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Python-openbabel
Chemical toolbox library (python bindings)
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Versions of package python-openbabel |
Release | Version | Architectures |
wheezy | 2.3.1+dfsg-4 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 2.3.2+dfsg-2 | amd64,armel,armhf,i386 |
stretch | 2.3.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 2.2.3-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
buster | 2.4.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 3.0.0 |
Debtags of package python-openbabel: |
devel | lang:python |
field | chemistry |
role | shared-lib |
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License: DFSG free
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Open Babel is a chemical toolbox designed to speak the many languages of
chemical data. It allows one to search, convert, analyze, or store data from
molecular modeling, chemistry, solid-state materials, biochemistry, or related
areas. Features include:
- Hydrogen addition and deletion
- Support for Molecular Mechanics
- Support for SMARTS molecular matching syntax
- Automatic feature perception (rings, bonds, hybridization, aromaticity)
- Flexible atom typer and perception of multiple bonds from atomic coordinates
- Gasteiger-Marsili partial charge calculation
File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL
Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.
This package contains the Python binding.
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Python-rdkit
Collection of cheminformatics and machine-learning software
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Versions of package python-rdkit |
Release | Version | Architectures |
wheezy | 201203-3 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 201403-1 | amd64,armel,armhf,i386 |
stretch | 201603.5-2 | amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 201809.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 201909.2 |
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License: DFSG free
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RDKit is a Python/C++ based cheminformatics and machine-learning software
environment. Features Include:
- Chemical reaction handling and transforms
- Substructure searching with SMARTS
- Canonical SMILES
- Molecule-molecule alignment
- Large number of molecular descriptors, including topological,
compositional, EState, SlogP/SMR, VSA and Feature-map vectors
- Fragmentation using RECAP rules
- 2D coordinate generation and depiction, including constrained depiction
- 3D coordinate generation using geometry embedding
- UFF and MMFF94 forcefields
- Chirality support, including calculation of (R/S) stereochemistry codes
- 2D pharmacophore searching
- Fingerprinting, including Daylight-like, atom pairs, topological
torsions, Morgan algorithm and MACCS keys
- Calculation of shape similarity
- Multi-molecule maximum common substructure
- Machine-learning via clustering and information theory algorithms
- Gasteiger-Marsili partial charge calculation
File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit
binary format.
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